[9] BGI Research, the group's nonprofit division, works with the Institute of Genomics and operates the China National GeneBank under a contract with the Chinese government.

[15] Wang Jian, Yu Jun, Yang Huanming and Liu Siqi created BGI, originally named Beijing Genomics Institute, in September 1999,[16] in Beijing, China as a non-governmental independent research institute in order to participate in the Human Genome Project as China's representative.

[17][22] In 2010, BGI bought 128 Illumina HiSeq 2000 gene-sequencing machines,[3][17] which was backed by US$1.5 billion in "collaborative funds" over the next 10 years from the state lender China Development Bank.

[32] That year they also launched their own scientific journal, GigaScience,[33] partnering with BioMed Central to publish data-heavy life science papers.

[35][36] In 2013, BGI bought Complete Genomics of Mountain View, California, a major supplier of DNA sequencing technology, for US$118 million, after gaining approval from the Committee on Foreign Investment in the United States.

[38] In 2015, BGI signed a collaboration with the Zhongshan Hospital' Center for Clinical Precision Medicine in Shanghai, opened in May 2015 with a budget of ¥100 million.

[3][39] In May 2017, was announced formation of West Coast Innovation Center, co-located in Seattle and San Jose, on the first location planned to work on precision medicine and feature collaborations with University of Washington, the Allen Institute for Brain Science, the Bill & Melinda Gates Foundation, and Washington State University, while on the second's already existing laboratory with 100 employees to develop the next-generation sequencing technologies.

[42] In 2019, it was reported that a BGI subsidiary, Forensic Genomics International, had created a WeChat-enabled database of genetic profiles of people across the country.

[48] In 2021, state-owned enterprises of State Development and Investment Corporation and China Merchants Group took ownership stakes in BGI Genomics.

[49] In July 2020, the United States Department of Commerce's Bureau of Industry and Security placed two BGI subsidiaries on its Entity List for assisting in alleged human rights abuses due to its genetic analysis work in Xinjiang.

[55] In 2011, BGI sequenced the genome of E. coli bacteria causing an epidemic in Europe to identify genes that lead to resistance to antibiotics.

The government of California rejected the offer due to geopolitical concerns, but Santa Clara County did buy COVID-19 test kits and equipment from BGI.

[59] On August 25, 2020, Reuters reported that about 3,700 people in Sweden were told in error that they had the coronavirus due to a fault in a COVID-19 testing kit from BGI Genomics.

[76][77] In 2022, BGI-Research and University of Chinese Academy of Sciences together with scientists globally, used sequencing technologies to undertake single cell sequencing to expand the understanding of early human embryonic development, to complete the first whole-body cell atlas of a non-human primate, to complete the world's first body-wide single cell transcriptome atlas of pigs, and to study the brains of ants to explain for the first time how the social division of labor within ant colonies is determined by functional specialization of their brains at cellular levels.

[91][92] In response, BGI has filed patent infringement lawsuits against Illumina alleging violations of federal antitrust and California unfair competition laws.

[96] In January 2021, Reuters reported that BGI has worked with the People's Liberation Army (PLA) and affiliated institutions such as the National University of Defense Technology on efforts to enhance soldiers' strength and other projects.

[97] In July 2021, Reuters reported that BGI developed a prenatal test, with the assistance of the People's Liberation Army, which is also used for genetic data collection.

[100] In August 2021, the UK announced a registration requirement with the Medicines and Healthcare products Regulatory Agency for BGI's prenatal tests.

[102][103][104] In November 2021, Reuters reported that a University of Copenhagen professor, Guojie Zhang, who was also employed by BGI was developing drugs for the PLA to assist soldiers with managing altitude sickness.